Benjamin Mangkoedilaga, a commissioner for the Truth and Friendship Commission (TFC), which began work in August, said on Friday that the role of the commission is to determine the facts surrounding the 1999 bloodshed that left an estimated 1500 dead - not to prosecute suspects.
He said people who were in a position of authority when the violence broke out will be summoned before the 10-member commission from January to July, including General Wiranto, the former Indonesian armed forces chief, who has denied any wrongdoing.
Mangkoedilaga said at a press conference: "Clearly, Wiranto's position will be examined."
East Timor overwhelmingly voted for independence in 1999, which ended 24 years of Indonesian rule.
About half of East Timor's 700,000 people fled their homes during the violence preceding elections, which ended with the arrival of peacekeeping troops.
The five Indonesian and five East Timorese commission members have for months been looking at documents from previous investigations and an Indonesian human rights court, which failed to hand down a single sentence for any of the 18 people charged.
After questioning witnesses, who can provide written testimonies if they do not want to appear in person, the commission will issue a report for the East Timorese and Indonesian governments describing the cause of the violence.
"We are not a judicial body and don't have judicial powers. The government will decide what to do with our recommendations"
member of the Truth and Friendship Commission
Indonesia has resisted international pressure for a full-blown international tribunal with the power to try perpetrators of the violence - such as those held for Rwanda and the Balkans.
East Timor has agreed, saying it does not want to jeopardise bilateral relations.
Not a judicial body
Achmad Ali, another member of the commission, stressing that the commission will not take any legal action, said: "We are not a judicial body and don't have judicial powers. The government will decide what to do with our recommendations."
The two governments formed the joint TFC, which is made up of lawyers, judges and human rights workers from both countries.
However, critics say it is an attempt to absolve Indonesia's generals of responsibility for crimes committed in East Timor.